N6-methyladenosine (m6A Individual-Nucleotide-Resolution Crosslinking and Immunoprecipitation miCLIP-m6A maps m6A locations in the transcriptome with single-nucleotide resolution (Linder et al., 2015). In this method, anti-m6A antibodies are crosslinked to mRNA sequences, and a cDNA library is prepared and sequenced. The cDNA library preparation in miCLIP follows […]

m6A-Specific Methylated RNA Immunoprecipitation Sequencing MeRIP-Seq maps m6A-methylated RNA. In this method, m6A-specific antibodies are used to immunoprecipitate RNA. RNA is reverse-transcribed to cDNA and sequenced. Deep sequencing provides high-resolution reads of m6A-methylated RNA (Meyer et al., 2012)Similar methods: miCLIP, m6A-LAIC-SeqAdvantages: Maps m6A-methylated RNADisadvantages: Antibodies […]

Inosine Chemical Erasing ICE (Sakurai et al., 2010) (Sakurai et al., 2014) (Suzuki et al., 2015) followed by NGS identifies adenosine-to-inosine editing. In this method, RNA is treated with acrylonitrile, while control RNA is untreated. Control and treated RNAs are reverse-transcribed and PCR-amplified. Inosines in […]

All of the RNA Modification sequencing methods are collected together under this heading

Unique Molecular Identifiers Unique molecular identifiers (UMI) are molecular tags that are used to detect and quantify unique mRNA transcripts (Kivioja et al., 2012). In this method, mRNA libraries are generated by fragmentation and reverse-transcribed to cDNA. Oligo(dT) primers with specific sequencing linkers are added […]

Transcriptome in Vivo Analysis TIVA is a protocol that captures mRNA from live cells (Lovatt et al., 2014). In this method, a photoactivatable TIVA tag is loaded into cells. Selective photoactivation exposes the mRNA-capturing portion of the tag, allowing it to hybridize to the poly(A) […]

TCR Ligation-Anchored Magnetically Captured PCR TCR-LA-MC PCR identifies TCR-_ and -_ chains from T cells and uses sequencing to analyze the catalog of clonal TCR in vivo or in vitro from blood or tissue samples (Ruggiero et al., 2015). This technique can be performed with […]

Single-Cell Universal Poly(A)-Independent RNA Sequencing SUPeR-Seq sequences non-poly(A) and poly(A) RNAs from single cells. It is designed particularly for mapping circular RNA (circRNA) species (Fan et al., 2015). RNA samples from lysed single cells are annealed to random primers with universal anchor sequences (AnchorX-T15N6) and […]

Single-Cell Tagged Reverse Transcription Sequencing STRT-Seq is a method similar to CEL-Seq that involves unique barcoding and sample pooling to overcome the challenges of samples with limited material (Islam et al., 2011) (Islam et al., 2012). In this method, single cells are first picked in […]

Single-Nuclei RNA Sequencing snRNA-Seq uses a mild and quick nuclear dissociation protocol to isolate and sequence RNA within the nucleus. The method minimizes technical issues that can arise from common dissociation protocols, especially in studying immediate early gene (IEG) behavior (Lacar et al., 2016). In […]